I am trying to find the explanation for a dilemma I came across during some RNA-seq data analysis.
I noticed that switching between
-t exon and
-t gene in featureCounts highly affects the output read counts for certain genes.
For example, some housekeeping genes gave the expected high read counts across all samples when using
-t exon, while when using
-t gene read counts went either to 0 or to very low values close to 0.
I can't fully understand why so, since I expect that
-t gene should also include exons in the annotation procedure.
I appreciate any comments in this regard.